Software tools for statistical analysis arid comparison of proteomics data is proposed. Using these tools, data can be compared from different research groups using different experimental techniques, analytical instrumentation, peptide search engines, and databases. Proteomics can produce human health breakthroughs, but progress is hampered by the inability to directly compare and integrate results from different experiments. The proposed solution is a set of software tools permitting peptide identifications to be compared in a statistically-valid way, and permitting data to be readily exchanged between research groups. The research team includes leading experts in peptide search, proteomics databases, analysis of multidimensional chromatography, and scientific computing. The group has developed an extensive suite of proteomics software, which forms the foundation for this research. Collaborations give the team access to data from leading-edge proteomics experiments. Working with consortium partners, a heterogeneous proteomics data analysis and management system will be developed, base primarily on proteomics tools developed at the Institute for Systems Biology. We will extend the tools to support additional equipment and software systems, develop an integrated framework, and develop training materials and documentation. This system will be applicable to a range of proteomics analysis experiments, accelerating the adoption of new proteomics analysis techniques.